Package pipestat Documentation
Class PipestatError
Base exception type for this package
Class SamplePipestatManager
Pipestat standardizes reporting of pipeline results and pipeline status management. It formalizes a way for pipeline developers and downstream tools developers to communicate -- results produced by a pipeline can easily and reliably become an input for downstream analyses. A PipestatManager object exposes an API for interacting with the results and pipeline status and can be backed by either a YAML-formatted file or a database.
def __init__(self, **kwargs)
Initialize the PipestatManager object
Parameters:
record_identifier(str): record identifier to report for. Thiscreates a weak bound to the record, which can be overridden in this object method callsschema_path(str): path to the output schema that formalizesthe results structureresults_file_path(str): YAML file to report into, if file isused as the object back-enddatabase_only(bool): whether the reported data should not bestored in the memory, but only in the databaseconfig_file(str): path to the configuration fileconfig_dict(dict): a mapping with the config file contentflag_file_dir(str): path to directory containing flag filesshow_db_logs(bool): Defaults to False, toggles showing database logspipeline_type(str): "sample" or "project"pipeline_name(str): name of the current pipeline, defaults toresult_formatter(str): function for formatting resultmulti_pipelines(bool): allows for running multiple pipelines for one file backendoutput_dir(str): target directory for report generation via summarize and table generation via table.
def clear_status(self, *args, **kwargs)
def config_path(self)
Config path. None if the config was not provided or if provided as a mapping of the config contents
Returns:
str: path to the provided config
def count_records(self, *args, **kwargs)
def data(self)
Data object
Returns:
yacman.YAMLConfigManager: the object that stores the reported data
def db_url(self)
Database URL, generated based on config credentials
Returns:
str: database URL
Raises:
PipestatDatabaseError: if the object is not backed by a database
def file(self)
File path that the object is reporting the results into
Returns:
str: file path that the object is reporting the results into
def get_status(self, *args, **kwargs)
def highlighted_results(self)
Highlighted results
Returns:
List[str]: a collection of highlighted results
def initialize_dbbackend(*args, **kwargs)
def link(self, *args, **kwargs)
def list_recent_results(self, *args, **kwargs)
def output_dir(self)
Output directory for report and stats generation
Returns:
str: path to output_dir
def pipeline_name(self)
Pipeline name
Returns:
str: Pipeline name
def pipeline_type(self)
Pipeline type: "sample" or "project"
Returns:
str: pipeline type
def project_name(self)
Project name the object writes the results to
Returns:
str: project name the object writes the results to
def record_count(self)
Number of records reported
Returns:
int: number of records reported
def record_identifier(self)
Pipeline type: "sample" or "project"
Returns:
str: pipeline type
def remove(self, *args, **kwargs)
def report(self, *args, **kwargs)
def result_schemas(self)
Result schema mappings
Returns:
dict: schemas that formalize the structure of each resultin a canonical jsonschema way
def retrieve_one(self, *args, **kwargs)
def schema(self)
Schema mapping
Returns:
ParsedSchema: schema object that formalizes the results structure
def schema_path(self)
Schema path
Returns:
str: path to the provided schema
def select_distinct(self, *args, **kwargs)
def select_records(self, *args, **kwargs)
def set_status(self, *args, **kwargs)
def status_schema(self)
Status schema mapping
Returns:
dict: schema that formalizes the pipeline status structure
def status_schema_source(self)
Status schema source
Returns:
dict: source of the schema that formalizesthe pipeline status structure
def summarize(self, *args, **kwargs)
def table(self, *args, **kwargs)
Class ProjectPipestatManager
Pipestat standardizes reporting of pipeline results and pipeline status management. It formalizes a way for pipeline developers and downstream tools developers to communicate -- results produced by a pipeline can easily and reliably become an input for downstream analyses. A PipestatManager object exposes an API for interacting with the results and pipeline status and can be backed by either a YAML-formatted file or a database.
def __init__(self, **kwargs)
Initialize the PipestatManager object
Parameters:
record_identifier(str): record identifier to report for. Thiscreates a weak bound to the record, which can be overridden in this object method callsschema_path(str): path to the output schema that formalizesthe results structureresults_file_path(str): YAML file to report into, if file isused as the object back-enddatabase_only(bool): whether the reported data should not bestored in the memory, but only in the databaseconfig_file(str): path to the configuration fileconfig_dict(dict): a mapping with the config file contentflag_file_dir(str): path to directory containing flag filesshow_db_logs(bool): Defaults to False, toggles showing database logspipeline_type(str): "sample" or "project"pipeline_name(str): name of the current pipeline, defaults toresult_formatter(str): function for formatting resultmulti_pipelines(bool): allows for running multiple pipelines for one file backendoutput_dir(str): target directory for report generation via summarize and table generation via table.
def clear_status(self, *args, **kwargs)
def config_path(self)
Config path. None if the config was not provided or if provided as a mapping of the config contents
Returns:
str: path to the provided config
def count_records(self, *args, **kwargs)
def data(self)
Data object
Returns:
yacman.YAMLConfigManager: the object that stores the reported data
def db_url(self)
Database URL, generated based on config credentials
Returns:
str: database URL
Raises:
PipestatDatabaseError: if the object is not backed by a database
def file(self)
File path that the object is reporting the results into
Returns:
str: file path that the object is reporting the results into
def get_status(self, *args, **kwargs)
def highlighted_results(self)
Highlighted results
Returns:
List[str]: a collection of highlighted results
def initialize_dbbackend(*args, **kwargs)
def link(self, *args, **kwargs)
def list_recent_results(self, *args, **kwargs)
def output_dir(self)
Output directory for report and stats generation
Returns:
str: path to output_dir
def pipeline_name(self)
Pipeline name
Returns:
str: Pipeline name
def pipeline_type(self)
Pipeline type: "sample" or "project"
Returns:
str: pipeline type
def project_name(self)
Project name the object writes the results to
Returns:
str: project name the object writes the results to
def record_count(self)
Number of records reported
Returns:
int: number of records reported
def record_identifier(self)
Pipeline type: "sample" or "project"
Returns:
str: pipeline type
def remove(self, *args, **kwargs)
def report(self, *args, **kwargs)
def result_schemas(self)
Result schema mappings
Returns:
dict: schemas that formalize the structure of each resultin a canonical jsonschema way
def retrieve_one(self, *args, **kwargs)
def schema(self)
Schema mapping
Returns:
ParsedSchema: schema object that formalizes the results structure
def schema_path(self)
Schema path
Returns:
str: path to the provided schema
def select_distinct(self, *args, **kwargs)
def select_records(self, *args, **kwargs)
def set_status(self, *args, **kwargs)
def status_schema(self)
Status schema mapping
Returns:
dict: schema that formalizes the pipeline status structure
def status_schema_source(self)
Status schema source
Returns:
dict: source of the schema that formalizesthe pipeline status structure
def summarize(self, *args, **kwargs)
def table(self, *args, **kwargs)
Class PipestatBoss
PipestatBoss simply holds Sample or Project Managers that are child classes of PipestatManager. :param list[str] pipeline_list: list that holds pipeline types, e.g. ['sample','project'] :param str record_identifier: record identifier to report for. This creates a weak bound to the record, which can be overridden in this object method calls :param str schema_path: path to the output schema that formalizes the results structure :param str results_file_path: YAML file to report into, if file is used as the object back-end :param bool database_only: whether the reported data should not be stored in the memory, but only in the database :param str | dict config: path to the configuration file or a mapping with the config file content :param str flag_file_dir: path to directory containing flag files :param bool show_db_logs: Defaults to False, toggles showing database logs :param str pipeline_type: "sample" or "project" :param str result_formatter: function for formatting result :param bool multi_pipelines: allows for running multiple pipelines for one file backend :param str output_dir: target directory for report generation via summarize and table generation via table.
def __init__(self, pipeline_list: Optional[list]=None, **kwargs)
Initialize self. See help(type(self)) for accurate signature.
Class PipestatManager
Pipestat standardizes reporting of pipeline results and pipeline status management. It formalizes a way for pipeline developers and downstream tools developers to communicate -- results produced by a pipeline can easily and reliably become an input for downstream analyses. A PipestatManager object exposes an API for interacting with the results and pipeline status and can be backed by either a YAML-formatted file or a database.
def __init__(self, project_name: Optional[str]=None, record_identifier: Optional[str]=None, schema_path: Optional[str]=None, results_file_path: Optional[str]=None, database_only: Optional[bool]=True, config_file: Optional[str]=None, config_dict: Optional[dict]=None, flag_file_dir: Optional[str]=None, show_db_logs: bool=False, pipeline_type: Optional[str]=None, pipeline_name: Optional[str]='default_pipeline_name', result_formatter: staticmethod=<function default_formatter at 0x71006ce003a0>, multi_pipelines: bool=False, output_dir: Optional[str]=None)
Initialize the PipestatManager object
Parameters:
record_identifier(str): record identifier to report for. Thiscreates a weak bound to the record, which can be overridden in this object method callsschema_path(str): path to the output schema that formalizesthe results structureresults_file_path(str): YAML file to report into, if file isused as the object back-enddatabase_only(bool): whether the reported data should not bestored in the memory, but only in the databaseconfig_file(str): path to the configuration fileconfig_dict(dict): a mapping with the config file contentflag_file_dir(str): path to directory containing flag filesshow_db_logs(bool): Defaults to False, toggles showing database logspipeline_type(str): "sample" or "project"pipeline_name(str): name of the current pipeline, defaults toresult_formatter(str): function for formatting resultmulti_pipelines(bool): allows for running multiple pipelines for one file backendoutput_dir(str): target directory for report generation via summarize and table generation via table.
def check_multi_results(self)
def clear_status(self, *args, **kwargs)
def config_path(self)
Config path. None if the config was not provided or if provided as a mapping of the config contents
Returns:
str: path to the provided config
def count_records(self, *args, **kwargs)
def data(self)
Data object
Returns:
yacman.YAMLConfigManager: the object that stores the reported data
def db_url(self)
Database URL, generated based on config credentials
Returns:
str: database URL
Raises:
PipestatDatabaseError: if the object is not backed by a database
def file(self)
File path that the object is reporting the results into
Returns:
str: file path that the object is reporting the results into
def get_status(self, *args, **kwargs)
def highlighted_results(self)
Highlighted results
Returns:
List[str]: a collection of highlighted results
def initialize_dbbackend(*args, **kwargs)
def initialize_filebackend(self, record_identifier, results_file_path, flag_file_dir)
def link(self, *args, **kwargs)
def list_recent_results(self, *args, **kwargs)
def output_dir(self)
Output directory for report and stats generation
Returns:
str: path to output_dir
def pipeline_name(self)
Pipeline name
Returns:
str: Pipeline name
def pipeline_type(self)
Pipeline type: "sample" or "project"
Returns:
str: pipeline type
def process_schema(self, schema_path)
def project_name(self)
Project name the object writes the results to
Returns:
str: project name the object writes the results to
def record_count(self)
Number of records reported
Returns:
int: number of records reported
def record_identifier(self)
Pipeline type: "sample" or "project"
Returns:
str: pipeline type
def remove(self, *args, **kwargs)
def report(self, *args, **kwargs)
def resolve_results_file_path(self, results_file_path)
Replace {record_identifier} in results_file_path if it exists.
Parameters:
results_file_path(str): YAML file to report into, if file isused as the object back-end
def result_schemas(self)
Result schema mappings
Returns:
dict: schemas that formalize the structure of each resultin a canonical jsonschema way
def retrieve_many(self, record_identifiers: List[str], result_identifier: Optional[str]=None) -> Union[Any, Dict[str, Any]]
Parameters:
record_identifiers(``): list of record identifiersresult_identifier(str): single record_identifier
Returns:
- ``: a mapping with filteredresults reported for the record
def retrieve_one(self, *args, **kwargs)
def schema(self)
Schema mapping
Returns:
ParsedSchema: schema object that formalizes the results structure
def schema_path(self)
Schema path
Returns:
str: path to the provided schema
def select_distinct(self, *args, **kwargs)
def select_records(self, *args, **kwargs)
def set_status(self, *args, **kwargs)
def status_schema(self)
Status schema mapping
Returns:
dict: schema that formalizes the pipeline status structure
def status_schema_source(self)
Status schema source
Returns:
dict: source of the schema that formalizesthe pipeline status structure
def summarize(self, *args, **kwargs)
def table(self, *args, **kwargs)
Version Information: pipestat v0.9.0a1, generated by lucidoc v0.4.4